4D74

1.57 A crystal structure of erwinia amylovora tyrosine phosphatase amsI


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2WMYPDB ENTRY 2WMY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1MICROBATCH5.5MICROBATCH UNDER OIL 1UL PROTEIN ADDED TO 1 UL AMMONIUM SULPHATE 1.7 M, 100MM SODIUM ACETATE PH 5.5.
Crystal Properties
Matthews coefficientSolvent content
2.7555.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.026α = 90
b = 66.026β = 90
c = 72.273γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-01-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.5772.271000.0623.219.725949216.85
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.571.61000.585.520.2

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2WMY1.5757.1824575131899.90.169340.168810.17922RANDOM23.483
Temperature Factor Modeling
Anisotropic B[1][1]Anisotropic B[1][2]Anisotropic B[1][3]Anisotropic B[2][2]Anisotropic B[2][3]Anisotropic B[3][3]
0.70.70.7-2.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.822
r_dihedral_angle_4_deg14.434
r_dihedral_angle_3_deg12.489
r_dihedral_angle_1_deg5.279
r_angle_refined_deg1.591
r_angle_other_deg0.806
r_chiral_restr0.092
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.822
r_dihedral_angle_4_deg14.434
r_dihedral_angle_3_deg12.489
r_dihedral_angle_1_deg5.279
r_angle_refined_deg1.591
r_angle_other_deg0.806
r_chiral_restr0.092
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1157
Nucleic Acid Atoms
Solvent Atoms100
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
BALBESphasing